The Amino Acid Molecular Weight Calculator estimates polypeptide molecular weight from residue count or sequence. Used in protein biochemistry, proteomics, and biopharmaceutical development for SDS-PAGE analysis, mass spectrometry interpretation, and molar concentration calculations.
16,540
Da
16.54
kDa
2,684.24
Da
16,540
Da
16.54
kDa
2,684.24
Da
The calculator for amino acid molecular weight estimates the molecular weight of a polypeptide from its amino acid composition or total residue count. Protein molecular weight is fundamental to biochemistry — determining migration on SDS-PAGE gels, interpreting mass spectrometry results, calculating molar concentrations from weight concentrations, and establishing biopharmaceutical dosing parameters.
Two molecular weight values are used depending on the analytical context:
The distinction becomes significant above approximately 2,000 Da — for a 50 kDa protein, the monoisotopic mass is approximately 50 Da lighter than the average mass. The protein molar conversion calculator converts between weight and molar concentrations using the calculated MW.
The molecular weight of a polypeptide is the sum of residue weights minus water lost during peptide bond formation, plus one water for the terminal groups: MW = Σ(residue weights) + 18.02. Average residue masses range from 57.05 Da (glycine) to 186.21 Da (tryptophan), with the average protein residue mass approximately 110–115 Da. For a 200-residue protein: approximate MW = 200 × 110 + 18 ≈ 22,018 Da = 22 kDa. Use this online calculator for both residue-count estimates and sequence-based exact calculations.
SDS-PAGE separates proteins by molecular weight under denaturing conditions. The logarithm of protein MW is approximately linear with migration distance, allowing unknown masses to be estimated by comparison with a molecular weight ladder. Calculated MW is used to predict migration position, verify recombinant protein expression, identify oligomeric states, and estimate preparation purity by densitometry. The extinction coefficient calculator uses MW alongside the molar extinction coefficient to convert absorbance at 280 nm into molar concentration.
Therapeutic proteins require precise molar concentration calculations for dosing. A monoclonal antibody IgG typically has MW of approximately 150 kDa. Converting a clinical dose of 5 mg/kg in a 70 kg patient (350 mg) to molar amount: 350 mg / 150,000 g/mol = 2.33 nmol. This molar conversion requires accurate MW determination — an error of 10% in MW translates directly to a 10% error in molar dose. The protein dilution calculator applies the calculated MW to concentration and dilution problems. The protein calculators provide the complete biochemistry toolkit.
The molecular weight calculation accounts for condensation (water loss) during peptide bond formation:
MW = N × avg_MW − (N − 1) × 18.015
Where:
The default 128.16 Da represents a typical protein composition. For glycine-rich proteins, use a lower value (~75 Da for pure glycine). For tryptophan-rich proteins, use a higher value (~204 Da for pure tryptophan).
Inputs
Results
A 150-amino acid polypeptide with average composition has a MW of approximately 16.5 kDa. The 149 peptide bonds account for 2,684 Da of water loss.
Inputs
Results
A glycine-rich collagen-like protein (avg MW ~95 Da/residue) with 300 residues has a MW of approximately 23.1 kDa, lower than the standard estimate would suggest.
The default 128.16 Da represents a typical mammalian protein composition. For proteins with known amino acid bias, adjust accordingly. Some common references: glycine-rich proteins (~75–90 Da average), standard composition (110–130 Da), aromatic-rich proteins (140–160 Da). For the most accurate estimate, calculate the weighted average from your actual amino acid composition, or use ExPASy ProtParam with the full sequence.
Peptide bond formation is a condensation (dehydration) reaction: the α-carboxyl group of one amino acid reacts with the α-amino group of the next, releasing one water molecule (H₂O, 18.015 Da). A polypeptide with N residues has (N−1) peptide bonds, so (N−1) water molecules are lost. Ignoring this correction overestimates MW by approximately 14% for a 100-residue protein.
This calculator provides a theoretical average MW based on composition. Mass spectrometry measures the actual monoisotopic or average mass of the intact protein, including all post-translational modifications (phosphorylation, glycosylation, acetylation, etc.), processing (signal peptide cleavage), and any bound cofactors or metal ions. The MS measurement is always more accurate than any calculation-based estimate.
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